In the graduate program in cell and molecular biology, the Ph.D. degree places great emphasis on rigorous, didactic preparation in cell biology, molecular biology, and genetics, and focuses on choosing questions, defining experimental approaches, and interpreting data. Once qualified, advanced students choose from a wider range of opportunities for research in cell biology, molecular biology, genetics, developmental biology, plant biology, and microbiology. Of special interest is the design of interdisciplinary programs that emphasize the frontiers of biology.

The Degree of Doctor of Philosophy

The graduate program in cell and molecular biology offers a program of study leading to the Doctor of Philosophy in molecular genetics and cell biology. A Ph.D. candidate must fulfill certain formal coursework requirements, pass one preliminary and one qualifying examination, and present a satisfactory dissertation describing the results of original research.

The program expects knowledge of and proficiency in cell biology, molecular biology, and genetics. This requirement will normally be met by fulfilling the formal coursework described here, but detailed degree programs are flexible. Courses taken at other institutions, in other departments, or as part of the Pritzker School of Medicine curriculum may substitute for CMB courses with approval of the curriculum committee. To fulfill the requirements for a Ph.D., nine graded courses are required. In the program in cell and molecular biology, a student must take one course in each of three areas during the first year:

Cell biology

Molecular biology

Genetics

In addition to these core courses, a second course in one of these areas is required to develop greater proficiency in a subdiscipline. The total of four required courses can be selected from among the following courses: MGCB 31200 Molecular Biology-I, MGCB 31300 Molecular Biology-II, MGCB 31400 Genetic Analysis of Model Organisms, MGCB 31600 Cell Biology I, and MGCB 31700 Cell Biology II. Three additional graded electives must be taken, one of which may be a reading course. The electives can be selected according to the student’s interests and the availability of courses.

A student is also required to do three laboratory rotations before selecting an advisor and laboratory to pursue a Ph.D. dissertation. These rotations will be graded, and two will count towards the nine courses required for the Ph.D. All students are required to serve as a teaching assistant for two quarters.

Students select a thesis advisor and begin laboratory research by the tenth month of the first year. To complete the Ph.D. degree, they must prepare, under the general direction of an appointed doctoral committee, a dissertation based upon their original research. Students are also required to submit, if not publish, at least one first author paper prior to their defense. A public seminar describing the results of the dissertation research must be presented and the dissertation must be successfully defended before the doctoral committee.

Molecular Genetics & Cell Biology Courses

MGCB 30400. Protein Fundamentals. 100 Units.

The course covers the physical and chemical phenomena that define protein structure and function. Topics include: the principles of protein folding, molecular motion and molecular recognition; protein evolution, design and engineering; enzyme catalysis; regulation of protein function and molecular machines; proteomics and systems biology. Workshop on X-ray Crystallography: The workshop is an addendum to Protein Fundamentals and is required for all BCMB students. This one-week workshop will provide students with an intensive introduction to protein structure determination by x-ray crystallography. In addition to lectures, an extensive laboratory component will give students the opportunity to carry out protein crystallization, data collection (at Argonne), structure determination, refinement, model building and validation.

Nucleic acid structure and DNA topology; methodology; nucleic-acid protein interactions; mechanisms and regulation of transcription in eubacteria, and of replication in eubacteria and eukaryotes; mechanisms of genome and plasmid segregation in eubacteria.

The content of this course covers the mechanisms and regulation of eukaryotic gene expression at the transcriptional and post-transcriptional levels. Our goal is to explore research frontiers and evolving methodologies. Rather than focusing on the elemental aspects of a topic, the lectures and discussions highlight the most significant recent developments, their implications and future directions. Enrollment requires the equivalent of an undergraduate molecular biology course or consent from the instructors.

Fundamental principles of genetics discussed in the context of current approaches to mapping and functional characterization of genes. The relative strengths and weaknesses of leading model organisms are emphasized via problem-solving and critical reading of original literature.

This course covers the mechanisms with which cells execute fundamental behaviors. Topics include signal transduction, cell cycle progression, cell growth, cell death, cancer biology, cytoskeletal polymers and motors, cell motility, cytoskeletal diseases, and cell polarity. Each lecture will conclude with a dissection of primary literature with input from the students. Students will write and present a short research proposal, providing excellent preparation for preliminary exams.

This course covers quantitative approaches to understanding biological organization and dynamics at molecular, sub-cellular and cellular levels. A key emphasis is on the use of simple mathematical models to gain insights into complex biological dynamics. We also will cover modern approaches to quantitative imaging and image analysis, and methods for comparing models to experimental data. A series of weekly computer labs will introduce students to scientific programming using Matlab and exercise basic concepts covered in the lectures.

This course explores specific ethical dilemmas that may arise in laboratory settings. The format of this course will provide opportunities for all students to voice their questions and opinions. Student groups of 4-5 will act as a review board during each session. Class time will center around the case, the conclusions of the review board, and the steps that should be taken to remedy the situation, if any. Faculty will guide and stimulate discussion in each case. Faculty will also provide any relevant University bylaws and/or NIH guidelines. Following the session, review board members will submit a formal 1-2 page justified decision in writing to the instructor. Successful completion of the course requires active participation in group presentations and general class discussions as well as joint submission of review board summaries.

Instructor(s): J. Malamy Terms Offered: Spring

MGCB 32300. Structure and Function of Membrane Proteins. 100 Units.

This course will be an in depth assessment of the structure and function of biological membranes. In addition to lectures, directed discussions of papers from the literature will be used. The main topics of the courses are: (1) Energetic and thermodynamic principles associated with membrane formation, stability and solute transport (2) membrane protein structure, (3) lipid-protein interactions, (4) bioenergetics and transmembrane transportmechanisms, and (5) specific examples of membrane protein systems and their function (channels, transporters, pumps, receptors). Emphasis will be placed on biophysical approaches in these areas. The primary literature will be the main source of reading.

This advanced-level course combines lectures, student presentations, and discussion sessions. It covers major topics on the developmental biology of embryos (e.g. formation of the germ line, gastrulation, segmentation, nervous system development, limb pattering, organogenesis). We make extensive use of the primary literature and emphasize experimental approaches including embryology, genetics, and molecular genetics.

Genetic approaches to central problems in plant development will be discussed. Emphasis will be placed on embryonic pattern formation, meristem structure and function, reproduction, and the role of hormones and environmental signals in development. Lectures will be drawn from the current literature; experimental approaches (genetic, cell biological, biochemical) used to discern developmental mechanisms will be emphasized. Graduate students will present a research proposal in oral and written form; undergraduate students will present and analyze data from the primary literature, and will be responsible for a final paper.

This course provides an overview of the fundamental questions of developmental biology, with particular emphasis on the genetic, molecular and cell biological experiments that have been employed to reach mechanistic answers to these questions. Topics covered will include formation of the primary body axes, the role of local signaling interactions in regulating cell fate and proliferation, the cellular basis of morphogenesis, and stem cells.